As thousands of students around the country rip open their GCSE results this morning, the gender debate that has been simmering for the last few years is set to ignite. Girls have beaten boys to the top grades for the past two decades: this year, boys are expected to narrow the gap.

In 1990, two years after GCSEs were introduced, 31% of boys achieved five A-C grades, compared with 38% of girls.

While girls still outperform boys in the number who get five A*-C grades, last year boys did better in maths for the first time in 12 years as a result of the decision to drop coursework entirely from maths GCSE. The proportion of boys getting grades A*-C in maths rose from 55.8% to 57.6% while the rate for girls stayed flat at 56.8%.

Last year, the then Department for Children, Schools and Families began replacing traditional coursework done at home with "controlled assessment" – coursework completed in exam conditions.

Controlled assessment was first unleashed on students of subjects including history, geography, French, Spanish, DT and business studies last September, so the GCSE grades out today are the first set of results under the new system.

From this coming academic year, English and IT will also be tested through controlled assessments rather than traditional coursework, while science subjects will follow suit in 2011. In time, only economics, law, religious studies, classical Greek, Latin, psychology and maths will allow students to avoid controlled assessments.

Therefore the impact of coursework changes will become far more significant over the next two years and experts reckon boys will benefit disproportionately. A 2009 report by the Higher Education Policy Institute (Hepi) compared GCSEs with their predecessor qualification, the O-level, which relied on exam assessment, and pinpointed coursework as a major factor behind boys' lower average grades at GCSE. At O-level, meanwhile, it was girls who traditionally fared worse.

"There is evidence that the introduction of GCSEs contributed to the deterioration in the relative participation of boys," the report concluded. "There are strong indications that the nature of the GCSE assessment (and the nature of the teaching and curriculum that feed it) is part of the reason for the relatively poor performance of boys." As a result, for 20 years, boys may have been "needlessly achieving less than they might".

"Girls often work better independently, and can be better at reflecting on teacher feedback, so in the past they have taken better advantage of coursework," said Nick Ward, deputy head of Treviglas school in Newquay, Cornwall. "Equally, they sometimes don't deal as well with assessment through exams as boys, who tend to be less hesitant at coming forward with their opinion and answers to questions.

"With the new assessment situations, that gender difference might kick in. I think girls may make the most of the opportunities to prepare for controlled assessments, which would limit the effect. But that will become clear over the next two years – we're still testing the waters."

Brittany Zeiderman, 16, who receives her GCSE results at North London Collegiate school in Edgware today, says having traditional coursework improved her English, history and art marks.

No pressure

"I think that where I did coursework, it bumped up my grades," she says. "During my coursework, there was no pressure of being timed during lessons. And being a girl who is easily distracted, I was glad to be able to isolate myself from friends and family and concentrate solidly on my work.

Michael Taylor, a GCSE student in year 11 at the Crypt grammar school in Gloucester, agrees. "It's difficult – your mind isn't fully on the work, you have the clock at the corner of your eye," he says. "Teachers watching you do the work adds a bit of pressure, so it's like being under exam conditions. I don't think it will really affect my grades, but I preferred being able to do coursework outside of school time."

But Mary Alice Grant, who has just finished year 11 at Joseph Swan school in Gateshead, liked doing supervised coursework for her GCSEs. "I felt happy that we didn't have to do coursework at home," she says. "At home, I could get easily distracted, whereas at school I can focus and stay on task. I think boys and girls are just as intelligent as each other, so the coursework switch is fair."

While teachers and students get to grips with the introduction of controlled assessment, more changes could be afoot. The examining body the Assessment and Qualifications Alliance (AQA) last week revealed that it is looking at plans to offer boys and girls different qualifications in the same subject, playing to different gender strengths.

But experts warn of the danger of such initiatives. Professor Sir John Holman, who helped to develop the science curriculum and is now director of the National Science Learning Centre, says no change in how students are examined should be taken lightly. "We have to be very, very careful to get both the style of the exams and their quality right," he says. "Playing around with exams or coursework can have an enormous effect on schools. While it's too early to say whether controlled assessment is better or worse for students, we know that getting it right is crucial."

This year's results, however, could see other factors coming into play. "With the current economic signals, and employment getting more difficult for young people, pupils and their parents are getting much more serious about GCSEs," says Holman. "But while girls have always tended to be more conscientious, boys are now concentrating their mind on what they need to get a decent job." This may also narrow the gender gap at GCSE, he says.

If boys start outperforming girls at GCSE, it will also have repercussions for higher education. The Hepi report suggested that the switch away from exam-only qualifications had led to women's dominance at university, where women now outperform men on almost every higher education indicator, and in most degree subjects. If boys start doing better at GCSE than girls, in the long term, female participation and performance in higher education could also decline.

The new GCSE results show foreign languages are in severe decline – with the number of children learning French and German falling most dramatically of all. Aida Edemariam asks what this means for our universities, our economy, and the future of Britain